ImagePlus2array_test.mlx

fijipath .... your Fiji.app/scripts folder path
close all;clear;clc
fijipath = getfijipath; %TODO getfijipath needs to be specified
addpath(fijipath);
ImageJ
-------------------------------------------------------------- Status> ImageJ is already running. --------------------------------------------------------------

8bit gray

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/AuPbSn40.jpg")
imp = img["AuPbSn40.jpg" (-5), 8-bit, 600x412x1x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[412 600]))
imshow(I)
imp.close()
imp = img["bat-cochlea-volume.tif" (-6), 8-bit, 121x154x1x114x1]

8 bit 4D

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/bat-cochlea-renderings.zip")
imp = img["bat-cochlea-renderings.tif" (-7), 8-bit, 284x154x1x36x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[154 284 1 36]))
imshow(I(:,:,1,1))
imp.close()
imp = img["blobs.gif" (-12), 8-bit, 256x254x1x1x1]

8bit gray

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif")
imp = img["boats.gif" (-50), 8-bit, 720x576x1x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[576 720]))
imshow(I)
imp.close()

RGB

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/cardio.dcm.zip")
imp = img["Cardio.dcm" (-51), 24-bit, 1000x1000x1x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[1000 1000 3]))
imshow(I)
imp.close()

RGB

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/clown.jpg")
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[200 320 3]))
imshow(I)
imp.close()

8 bit 4D, Hyperstack, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/confocal-series.zip")
imp = img["confocal-series.tif" (-77), 8-bit, 400x400x2x25x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[400 400 2 25]))
imshow(I(:,:,1,1,1))
imp.close()

16bit gray

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/ct.dcm.zip")
imp = img["ct.dcm.tif" (-81), 16-bit, 888x495x1x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[495 888]))
imshow(I)
set(gca,'CLimMode','auto')
imp.close()

3 channels, 8 bit, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/FluorescentCells.zip")
imp = img["FluorescentCells.tif" (-93), 8-bit, 512x512x3x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[512 512 3]))
imshow(I)
imp.close()

RGB, stack

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/flybrain.zip")
imp = img["flybrain.tif" (-124), 24-bit, 256x256x1x57x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint8'))
assert(isequal(size(I),[256 256 3 57]))
imshow(I(:,:,:,26))
imp.close()

16 bit,3 channels, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/hela-cells.zip")
imp = img["hela-cells.tif" (-133), 16-bit, 672x512x3x1x1]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[512 672 3]))
imshow(I(:,:,1))
set(gca,'ClimMode','auto')
imp.close()

16 bit, 5D, Hyperstack, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/Spindly-GFP.zip")
imp = img["mitosis.tif" (-147), 16-bit, 171x196x2x5x51]
imp.show();
imp.isHyperStack
imp.isComposite
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[196 171 2 5 51]))
imshow(I(:,:,1,3,25))
set(gca,'ClimMode','auto')
imp.close()

16 bit, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/Rat_Hippocampal_Neuron.zip")
imp = img["Rat_Hippocampal_Neuron.tif" (-172), 16-bit, 512x512x5x1x1]
imp.isHyperStack
ans = logical
0
imp.isComposite
ans = logical
1
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[512 512 5]))
imshow(I(:,:,1))
set(gca,'ClimMode','auto')
imp.close()

16 bit, Hyperstack, Composite

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/organ-of-corti.zip")
imp = img["organ-of-corti.tif" (-182), 16-bit, 548x249x4x15x1]
imp.isHyperStack
ans = logical
1
imp.isComposite
ans = logical
1
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[249 548 4 15]))
imshow(I(:,:,1,7))
set(gca,'ClimMode','auto')
imp.close()

16bit, 4D

imp = ij.IJ.openImage("http://imagej.nih.gov/ij/images/t1-head.zip")
imp = img["t1-head.tif" (-188), 16-bit, 256x256x1x129x1]
imp.isHyperStack
ans = logical
0
imp.isComposite
ans = logical
0
I = ImagePlus2array(imp);
assert(isequal(class(I),'uint16'))
assert(isequal(size(I),[256 256 1 129]))
imshow(I(:,:,1,60))
set(gca,'ClimMode','auto')
imp.close()